In general customising the server is a massive subject. Most things that you might want to alter (experience rates) are done so by editing the database tables, very little is done with actual files.
I would recommend downloading either HeidiSQL or Navicat to make it easy to see and edit your database, and a little research on databases in general if you're not familiar with them won't go amiss. The following link shows some of the things you can go onto and edit:-
http://wiki.eqemulator.org/p?Server_Rules&frm=Main